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GO::View is a Perl module that creates a gif or png image for visualizing the GO DAG.

This perl module generates a graphic that displays the parent and child relationships of a selected GO term. It also provides the visualization for the GO::TermFinder perl module created by the Stanford Microarray Database (SMD). This module is useful when analyzing experimental or computational results that produce a set of gene products that may have a common function or process.

SYNOPSIS

use GO::View;

my $goView =

GO::View->new(-goid => $goid,
-ontologyProvider => $ontology,
-annotationProvider => $annotation,
-termFinder => @pvalues,
-aspect => P,
-configFile => $confFile,
-imageDir => "/tmp",
-imageUrlRoot => "http://www.ABC.com/tmp",
-imageName => "GOview.88.png",
-tree => up,
-nodeUrl => $goUrl,
-geneUrl => $geneUrl,
-pvalueCutOff => 0.01,
-imageLabel => "SGD");


argument required expect data and type
-------------------------------------------------------------------------
-goid No A gene ontology ID (GOID).
If nothing is passed in, the module
will use the top goid of each ontology
branch (i.e, goid for
molecular_function, biological_process,
or cellular_component)

-ontologyProvider Yes An ontology provider instance.

-annotationProvider No An annotation provider instance. It is
required for creating tree for GO Term
Finder result.

-termFinder No An array of hash references returned
from findTerms method of
GO::TermFinder module. It is required
for creating tree for GO Term Finder
result.

-aspect No . The aspect of the ontology
provider. It is required for creating
tree for GO Term Finder result.

-configFile Yes The configuration file for setting the
general variables for the graphic
display.

-imageDir Yes The directory for storing the newly
created image file. It must be
world (nobody) readable and writable
if you want to display the image to
the web.

-imageUrlRoot No The url root for the -imageDir. It is
required if you want to display the
image to the web.

-imageName No The image file name. By default, the
name will be something like
GOview.xxxx.png. The xxxx will be
the process id. A suffix for the image (.png
or .gif) should not be provided, as that will
be determined at run time, depending on the
capabilities of the GD library.

-treeType No . The tree type.

1. up => display the ancestor tree
for the given goid.
2. down => display the descendant tree
for the given goid.
By default, it will display the
descendant tree.

-geneUrl No The URL for each Gene to link to.
It needs to have the text in
the url which will be substituted
by the real goid for a node.

-nodeUrl No The url for each GO node to link to.
It needs to have the text in
the url which will be substituted
by the real goid for a node.

-pvalueCutOff No The p-value cutoff for displaying
the graphic for GO Term Finder.
The default is 0.01

-imageLabel No The image label which will appear at
the left bottom corner of the map.
------------------------------------------------------------------------

To display the image on the web:

$goView->showGraph;

To create and return image file name with full path:

my $imageFile = $goView->createImage;

Java::Import::Design is the design of the Java::Import Module.

MOTIVATIONS

The original motivation for writing this module came out of a project I was working on during my previous employment. We had built a system in which a major part was implimented using EJBs on a J2EE server. In addition, we had a large component of the system, that already existed, and was written in Perl. We did not want to scrap our Perl work but it was becoming more tedious to maintain two implimentations as more and more things were being added to the system.

So, we decided that the major pieces of business logic would reside on the J2EE server and the Perl would be modified to make calls to the server. After some time and experimentation we began to realize that the memory footprint as well as the amount of time needed to make calls to the server using existing Perl to Java integration sulutions were just not acceptable. We therefore set out to find some other way. We tried all sorts of things but in the end we couldnt find anything that met our requirements and therefore decided to keep the origional system of doing things.

While at that job we never did find a suitable way to integrate our two systems. However, the problem still haunted me. It wasnt until the end of my career at that company that I saw an announcement for Googles first Summer of Code. It just so happened that as Google was announcing their brand new program that I had begun to play with the GNU GCJ suite of Java tools and came up with the idea of taking advantage of their ability to natively compile Java code for use with Perl. This may not have been a new idea but I couldnt find anything that would help me so I decided to write and submit a proposal to Google. Well, I was accepted and you now have Java::Import.

When I began to work on this project I started by creating my own namespace instead of stepping on the toes of the other existing Java/Perl integration project, Inline::Java. I did this primarily because I wanted a clean slate on which I could fully explore the nuances of GCJ, in particular its CNI interface. As I worked my module started to evolve into its own beast and at that point it seemed locigal to keep my own namespace. It is not my intention to replace Inline::Java and I still think that in te future much of the work I have done can be used by Inline::Java as an option to use GCJ specific functionality.

The system can be used in the electronic world to keep track of your: Schematic, Printed Circuit Board, Front Plate, Programmable Logic Device numbers.
EDA index is programmed in PHP (and XHTML 1.0), using a MySQL database to store data, so its more or less OS independent, but a Linux server is recommended, since it already got most software installed as default, this configuration is also called LAMP (Linux Apache MySQL PHP)
Its also recommended that a local intranet server is used, since the system dont got a user login, so all data can be viewed without a password, but when you need to add or edit data a password is required. At first this approach might seem wierd, but its designed to allow quick lookups. Example:
You are sitting with a broken pcb with a number on it, and need to find the schematic (so you can repair it) on the computer or in the printed project (schematic) archive. EDA Index allow an quick lookup in the database, without you needing to login, so you get the job done faster.
As far as I know, there are no commercial (or free) program available that can do what EDA Index can, some companies may have created their own software, but how do that help you.
I have worked in an electronic department that had a self made application, but it lagged features like search.
This program is very usefull, if you are using numbers when:
Drawing electronic Schematics and PCBs using a CAD program like: Eagle, gEDA, Protel, Orcad, etc.
Creating Front Plate layouts in: GIMP, Coral Draw, Photoshop, AutoCAD, etc.
Programming Programmable Logic Devices like: PLD, EPLD, CPLD, PIC, APIC, PEEL, PAL, GAL, FPGA, Intel 80XX, Motorola 68XX, etc. Writing the code in: VHDL, Assambler, JEDEC, etc.
Enhancements:
- Included the bugfix to RC2.
- Updated online documentation.
- Updated INSTALL file.

XView4Struts provides a Struts framework extension that replaces JSP pages with pure HTML.
The XView4Struts project is an extension to the Jakarta Struts Framework. Its main purpose is to eliminate the need to use tag libraries and JSP pages. The view is pure HTML, and interaction between the view and the model is transparent to the developer.
This approach offers faster development, better division of work, a more pure MVC design pattern, reusable view components, and easier maintenance.
With XView4Struts the view layer is pure HTML. This has several implications. You dont need a java developer to write HTML. Many organizations have graphics experts that are more suited for that job. Many organizations prefer to create HTML mock-ups of an application to solicit client approval before they start working on the underlying logic that makes it work. Using this scenerio with the standard Struts view layer, the developer then has to spend many hours implementing jsp tags to make it work with the underlying logic. With XView4Struts the developer only needs to apply id attributes to the standard HTML tags and the framework takes care of the rest.
XView4Struts extends the Struts requestProcessor and intercepts all forwarding actions to HTML pages. The processor parses the HTML page and if it can it will process any tags implementing an id attribute. If there is no match between the id attribute and a form bean property or an error occurs, the parser simply returns control back to the processor. Since only HTML pages are parsed, XView4Struts may exist in an application that implements the standard Struts view components.
Main features:
- Faster development time. A whole layer of programming has been removed since there are no JSPs to write. No tag libraries to learn and implement.
- Easier maintenance. There is no logic in the view layer to troubleshoot and maintain.
- A truer MVC design pattern since all logic in the view layer has been removed.
- The developer has an option to use xslt to produce dynamic content. Reusable view components are easy to build using this option. XView4Struts does not use xslt to produce the entire view layer as other implementations of this type do. It is only implemented to dynamically insert content pieces into the HTML document.
- Application templates are extremely easy to implement.
- The parsing functionality is dynamic enough that the developer often has more than one option or technology to choose from to achieve the same result. They simply use what they understand best.
Enhancements:
- Enhancement - Upgraded

Webesquema project is a PHP script that helps students/teachers to design diagrams.

The diagrams can be saved or printed, and support different styles (horizontal/vertical, colors, HTML, custom designs, etc.).